List of SEALS programs

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Note: system-dependent portions of the documentation are generated on the fly, so some sections of the static web documents may not agree with the documentation produced on your system.

man pages

gref
grefmatrix
grefre
rwidget

BLAST scripters

splat 
a BLAST scripter
  • splatp wusplatp splatpgp
  • splatn wusplatn splatngp
  • splatx wusplatx splatxgp
  • tsplatn twusplatn tsplatngp
  • tsplatx twusplatx tsplatxgp
splish 
a BLAST scripter
  • splishp wusplishp splishpgp
  • splishn wusplishn splishngp
  • splishx wusplishx splishxgp
  • tsplishn twusplishn tsplishngp
  • tsplishx twusplishx tsplishxgp
desplat 
clean up those messy splat searches


other scripters/wrappers

clustalify 
wrapper for ClustalW alignment/tree-building program
coilify 
wrapper for coils2 coiled-coil prediction by NCBI implementation
hmm_align 
wrapper for HMMER alignment programs
hmm_search 
database searches based on hidden markov models (wrapper for HMMer programs)
lupas_coilify 
wrapper for coils2 coiled-coil prediction by Lupas' implementation
phdify 
wrapper for PHD protein prediction
segify 
wrapper for SEG low-information domain detection
signalpify 
wrapper for signalP signal peptide prediction

BLAST result manipulation

blast2blast 
filter any kind of BLAST outputs by score, p : or e-value, etc.
blast2bounded 
extract HSPs / alignments from BLAST outputs
blast2gi 
convert BLAST results to lists or tables of hits
blast2filename 
convert BLAST results to lists or tables of hits
blast2header 
strip alignment/HSP data from BLAST files
gp2normal 
make gp variant outputs look more like old-style BLAST
psi2normal 
filter any kind of BLAST outputs by score, p : or e-value, etc.
shatterblast 
split/rename BLAST outputs according to query definition line

simple fasta file manipulation

assign_subversive_gis 
assign fake gi numbers to fasta records
columnize 
format fasta records into columns
daffy 
You must be taller than this script to ride this ride.
defkeys 
see the numbering of fasta defline fields
faand 
find the logical intersection between fasta libraries
faclean 
remove funny characters from fasta records
facount 
count the records in fasta libraries
fafilt 
filter out amino-acid or nucleic-acid sequences
faframe 
convert a nucleic acid sequence to various possible reading frames
faletters 
count the letters in fasta libraries
falower 
convert fasta records to lower case
faor 
find the logical union between fasta libraries
fanot 
find the logical difference between fasta libraries
fashuffle 
shuffle fasta records
fasort 
sort fasta libraries based on sequences or defline fields
fatweak 
tweak sequence boundaries
fauniq / nrify 
remove duplicate fasta records
faupper 
convert fasta records to upper case
faxor 
find the logical exclusive union between fasta libraries
fenestrate 
make windows on fasta records
gref 
match patterns in fasta libraries
mask_split 
split fasta records at masking boundaries
one2three 
convert single-letter amino acid codes to three-letter codes
remove_subversive_gis 
remove fake gi numbers from fasta records
select_defline 
select one of multiple deflines in fasta libraries
shatter 
split/rename fasta records based on the definition line
sieve 
remove long entries from fasta libraries
three2one 
convert three-letter amino acid codes to single-letter codes

GenBank flatfile manipulation

feature2fasta 
create fasta records from flatfile features

boundtable manipulation

blast2bounded 
extract HSPs / alignments from BLAST outputs
boundtable2fasta 
convert tables of sequence fragments into fasta libraries
compare_boundtable 
compare tables representing sequence fragments; find overlaps
merge_boundtable 
merge tables of sequence fragments
project_boundtable 
project normal and complement elements onto a single strand
split_boundtable 
split discontinuous sequence fragments
standardize_boundtable 
convert boundtables of different formats to the canonical SEALS format
strip_boundtable 
strip normal or complement elements from boundtables

Entrez retrieval

entrezping 
test your Entrez server
gi2abstract 
find abstracts associated with sequences
gi2fasta 
retrieve sequence data for a gi number
gi2genbank 
retrieve sequence data for a gi number
gi2asn1 
retrieve sequence data for a gi number
gi2defline 
retrieve sequence data for a gi number
gi2genbank_html 
retrieve sequence data for a gi number
genome2gi 
find all sequences from a systematic sequencing / mapping project
taxnode2amino_gi 
get all gis associated with a taxnode
taxnode2gi 
get all gis associated with a taxnode
taxnode2nucleic_gi 
get all gis associated with a taxnode

Netscape / html

hotbr 
html-ify BLAST outputs
hotgi 
hotlink gi numbers in any file
liftscape 
raise the current default Netscape window
peepscape 
grab the URL from a Netscape window
pipescape 
pipe a file into Netscape
pipescape_new 
pipe a file into Netscape
spitscape 
spit out the text from a Netscape window

pattern matching

gref 
match patterns in fasta libraries
grefd 
match patterns in fasta libraries
guess 
guess a pattern from an alignment
prosite2perl 
translates PROSITE-style regular expressions into Perl
prosite_as_perl 
search PROSITE by text word, returning perlish patterns

taxonomy analysis

tax_break 
summarize taxonomy data for a list of gi numbers
tax_collector 
summarize taxonomic identity of nearest homologs
tax_filt 
filter gi numbers according to taxonomy
tax_guess 
find an exact taxonomic name
tax_validate 
validate that the ranks in the taxonomy are consistent
taxnode2lineage 
see the lineage of any taxonomic node

unipred

coil_table 
create a table of predicted coiled-coil domains using ccp
seg_table 
create a table of predicted nonglobular domains using SEG
sig_table 
create a table of predicted signal peptides using SignalP
tm_table 
create a table of predicted transmembrane domains using PHD
unipred 
predict structural domains

general converters/extractors

boundtable2fasta 
convert tables of sequence fragments into fasta libraries
blastalign2fasta 
convert blast alignments to aligned fasta records
block2fasta 
convert aligned sequence blocks to aligned fasta records
clustalign2fasta / clustal2fasta 
convert CLUSTALW alignments into aligned fasta format
defline2gi 
extract gi numbers from the deflines of fasta records
fasta2clustalign 
convert aligned fasta records to CLUSTALW format.
fasta2defline 
extract the definition lines of fasta records
fasta2gi 
extract gi numbers from the deflines of fasta records
fasta2phylip 
convert aligned fasta records to PHYLIP format.
fasta2selex 
convert aligned fasta records to SELEX format.
fasta2seqrows 
convert fasta records to sequence rows
fastalign2fasta 
remove special delimiters from aligned fasta records.
fastalign2hmm 
convert aligned fasta records into a format compatible with HMMER
genbank2gi 
extract gi numbers from GenBank records
hmm2gi 
extract gi numbers from HMMER searches
hmmalign2fasta 
convert HMMER alignments into aligned fasta records
macaw2fasta 
convert MACAW alignments into aligned fasta format
most2gi 
extract gi numbers from MoST outputs
phylip2fasta 
convert PHYLIP alignments to aligned fasta records
selex2fasta 
convert SELEX alignments into aligned fasta format
seqrows2fasta 
convert sequences from sequence-row format to fasta records

miscellaneous functions

agree 
create a consensus sequence from an alignment
casealign2count 
substitute length values for unaligned regions in alignments
deindex 
cleans up index files created by fasta2index
fasta2index 
make indexes of fasta libraries for fast retrieval
famask 
mask fasta libraries based on predicted structural domains
gap_cds 
insert gaps in nucleotide sequence based on amino-acid alignments
gi2sibling 
find siblings for nucleotide and protein records
grouper 
group sequences by similarity scores
purger 
group sequences by similarity scores
wimklein 
a versatile translator
wubwub 
find duplications within a sequence

administration

seals 
examine your SEALS status
update_blastgp 
update BLAST-GP from the NCBI ftp site
update_gi_lists 
update retrieval hints from the NCBI ftp site
update_modules 
update Perl modules from a CPAN site
update_perlpath 
set the correct perl interpreter for SEALS scripts
update_permissions 
set permissions and links for your SEALS installation
update_prosite 
update the local PROSITE database from the Expasy web site
update_seg 
update SEG from the NCBI ftp site
update_taxonomy 
updates the local taxonomy databases from the NCBI ftp site
update_wublast 
update WU-BLAST from the Washington University ftp site

generic scripters

foreach_blast 
run a command on a series of BLAST results
foreach_fasta 
run a command on a series of fasta records
foreach_file 
run a command on a series of directories
foreach_genbank 
run a command on a series of GenBank-style flatfiles
foreach_dir 
run a command on a series of directories
foreach_line 
run a command on a series of lines
foreach_paragraph 
run a command on a series of empty line-delimited paragraphs
foreach_word 
run a command on a series of words

general utilities

bert 
a cat, with enormous globs
dupedupe 
find duplicate lines
mailme 
send a note to myself
nemp 
n e match print
pathadd 
add/remove path elements
plainwhich 
simple 'which' replacement
sortby 
sort lines according to a reference set
uniquniq 
create files of unique lines
singsing 
find unduplicated lines
stack_paragraphs 
stack paragraphs onto single lines
unstack_paragraphs 
unstack single lines into paragraphs

logical operations

and 
find the logical intersection between lines in files
not / nor 
find the logical difference between lines in files
or 
find the logical union between lines in files
xor 
find the logical exclusive union between lines in files
faand 
find the logical intersection between fasta libraries
fanot 
find the logical difference between fasta libraries
faor 
find the logical union between fasta libraries
faxor 
find the logical exclusive union between fasta libraries